function [jac,err] = jacobianest(fun,x0,t)
% gradest: estimate of the Jacobian matrix of a vector valued function of n variables
% usage: [jac,err] = jacobianest(fun,x0)
%
% 
% arguments: (input)
%  fun - (vector valued) analytical function to differentiate.
%        fun must be a function of the vector or array x0.
% 
%  x0  - vector location at which to differentiate fun
%        If x0 is an nxm array, then fun is assumed to be
%        a function of n*m variables.
%
%
% arguments: (output)
%  jac - array of first partial derivatives of fun.
%        Assuming that x0 is a vector of length p
%        and fun returns a vector of length n, then
%        jac will be an array of size (n,p)
%
%  err - vector of error estimates corresponding to
%        each partial derivative in jac.
%
%
% Example: (nonlinear least squares)
%  xdata = (0:.1:1)';
%  ydata = 1+2*exp(0.75*xdata);
%  fun = @(c) ((c(1)+c(2)*exp(c(3)*xdata)) - ydata).^2;
%
%  [jac,err] = jacobianest(fun,[1 1 1])
%
%  jac =
%           -2           -2            0
%      -2.1012      -2.3222     -0.23222
%      -2.2045      -2.6926     -0.53852
%      -2.3096      -3.1176     -0.93528
%      -2.4158      -3.6039      -1.4416
%      -2.5225      -4.1589      -2.0795
%       -2.629      -4.7904      -2.8742
%      -2.7343      -5.5063      -3.8544
%      -2.8374      -6.3147      -5.0518
%      -2.9369      -7.2237      -6.5013
%      -3.0314      -8.2403      -8.2403
%
%  err =
%   5.0134e-15   5.0134e-15            0
%   5.0134e-15            0   2.8211e-14
%   5.0134e-15   8.6834e-15   1.5804e-14
%            0     7.09e-15   3.8227e-13
%   5.0134e-15   5.0134e-15   7.5201e-15
%   5.0134e-15   1.0027e-14   2.9233e-14
%   5.0134e-15            0   6.0585e-13
%   5.0134e-15   1.0027e-14   7.2673e-13
%   5.0134e-15   1.0027e-14   3.0495e-13
%   5.0134e-15   1.0027e-14   3.1707e-14
%   5.0134e-15   2.0053e-14   1.4013e-12
%
%  (At [1 2 0.75], jac should be numerically zero)
%
%
% See also: derivest, gradient, gradest
%
%
% Author: John D'Errico
% e-mail: woodchips@rochester.rr.com
% Release: 1.0
% Release date: 3/6/2007
% get the length of x0 for the size of jac
nx = numel(x0);
MaxStep = 100;
StepRatio = 2.0000001;
% was a string supplied?
if ischar(fun)
  fun = str2func(fun);
end
% get fun at the center point
f0 = fun(x0,t);
f0 = f0(:);
n = length(f0);
if n==0
  % empty begets empty
  jac = zeros(0,nx);
  err = jac;
  return
end
relativedelta = MaxStep*StepRatio .^(0:-1:-25);
nsteps = length(relativedelta);
% total number of derivatives we will need to take
jac = zeros(n,nx);
err = jac;
for i = 1:nx
  x0_i = x0(i);
  if x0_i ~= 0
    delta = x0_i*relativedelta;
  else
    delta = relativedelta;
  end
  
  % evaluate at each step, centered around x0_i
  % difference to give a second order estimate
  fdel = zeros(n,nsteps);
  for j = 1:nsteps
    fdif = fun(swapelement(x0,i,x0_i + delta(j)),t) - ...
      fun(swapelement(x0,i,x0_i - delta(j)),t);
    
    fdel(:,j) = fdif(:);
  end
  
  % these are pure second order estimates of the
  % first derivative, for each trial delta.
  derest = fdel.*repmat(0.5 ./ delta,n,1);
  
  % The error term on these estimates has a second order
  % component, but also some 4th and 6th order terms in it.
  % Use Romberg exrapolation to improve the estimates to
  % 6th order, as well as to provide the error estimate.
  
  % loop here, as rombextrap coupled with the trimming
  % will get complicated otherwise.
  for j = 1:n
    [der_romb,errest] = rombextrap(StepRatio,derest(j,:),[2 4]);
    
    % trim off 3 estimates at each end of the scale
    nest = length(der_romb);
    trim = [1:3, nest+(-2:0)];
    [der_romb,tags] = sort(der_romb);
    der_romb(trim) = [];
    tags(trim) = [];
    
    errest = errest(tags);
    
    % now pick the estimate with the lowest predicted error
    [err(j,i),ind] = min(errest);
    jac(j,i) = der_romb(ind);
  end
end
end % mainline function end
% =======================================
%      sub-functions
% =======================================
function vec = swapelement(vec,ind,val)
% swaps val as element ind, into the vector vec
vec(ind) = val;
end % sub-function end
% ============================================
% subfunction - romberg extrapolation
% ============================================
function [der_romb,errest] = rombextrap(StepRatio,der_init,rombexpon)
% do romberg extrapolation for each estimate
%
%  StepRatio - Ratio decrease in step
%  der_init - initial derivative estimates
%  rombexpon - higher order terms to cancel using the romberg step
%
%  der_romb - derivative estimates returned
%  errest - error estimates
%  amp - noise amplification factor due to the romberg step
srinv = 1/StepRatio;
% do nothing if no romberg terms
nexpon = length(rombexpon);
rmat = ones(nexpon+2,nexpon+1);
% two romberg terms
rmat(2,2:3) = srinv.^rombexpon;
rmat(3,2:3) = srinv.^(2*rombexpon);
rmat(4,2:3) = srinv.^(3*rombexpon);
% qr factorization used for the extrapolation as well
% as the uncertainty estimates
[qromb,rromb] = qr(rmat,0);
% the noise amplification is further amplified by the Romberg step.
% amp = cond(rromb);
% this does the extrapolation to a zero step size.
ne = length(der_init);
rhs = vec2mat(der_init,nexpon+2,ne - (nexpon+2));
rombcoefs = rromb\(qromb'*rhs);
der_romb = rombcoefs(1,:)';
% uncertainty estimate of derivative prediction
s = sqrt(sum((rhs - rmat*rombcoefs).^2,1));
rinv = rromb\eye(nexpon+1);
cov1 = sum(rinv.^2,2); % 1 spare dof
errest = s'*12.7062047361747*sqrt(cov1(1));
end % rombextrap
% ============================================
% subfunction - vec2mat
% ============================================
function mat = vec2mat(vec,n,m)
% forms the matrix M, such that M(i,j) = vec(i+j-1)
[i,j] = ndgrid(1:n,0:m-1);
ind = i+j;
mat = vec(ind);
if n==1
  mat = mat';
end
end % vec2mat
